Functional Genomics Experiment (FuGE)

FuGE has been created to facilitate the development of data standards for functional genomics experiments.

Description

Functional Genomics Experiment (FuGE) - the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards for functional genomics experiments. FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways:

  • FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure.
  • FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow.

URLs:

http://fuge.sourceforge.net/index.php

Type

Data exchange format

Stage of Maturity

  • Emerging/Existing
  • FuGE version 1 final was released mid 2007

Producer

Contributors to FuGE development:

  • University of Pennsylvania, USA
  • University of Manchester, UK
  • Lawrence Berkeley National Laboratory, University of California
  • Rosetta Inpharmatics, LLC, USA
  • MGED Society
  • Proteomics Standards Initiative (PSI)
  • Fred Hutchinson Cancer Research Centre
  • Genologics
  • Friedrich Miescher Institute for Biomedical Research, Switzerland
  • Newcastle University, UK
  • University of Liverpool, UK

Maintainer

Association maintained - managed by a collaborative group from the above organizations

Users

Association use - FuGE is being used by the following organisations for data format development:

Support

Comments

  • Nature Biotechnology article about FuGE - 10/07

  • FuGE is closely related to other efforts including:

    • OBI(Ontology for Biological Investigations)
    • RSBI (Reporting Structures for Biological Information)

Examples

list of Sample Files

Tools

FuGE XSD-STK - software toolkit for FuGE XML Schema generation

Maturity Estimate: 
Emerging
Posted July 23rd, 2008 by agale
in